Pink News reports 37-year-old Jill Young left after three years of working at Dundonald school in Northern Ireland, accusing the principal of bullying and harassing her.
Young alleged that when the principal and vice-principal of the school discovered she was a lesbian, they treated her worse than other staff members and bullied her.
She claimed that the principal suggested she should leave and that unfounded complaints had been made about her work.
The South Eastern Education and Library Board has agreed to give her a Â£15,000 payout without admitting liability.
The board said it was committed to equality but would not comment on individual cases.